Correction of batch effects with BEclear as a command line tool. If you have any issues regarding the core program, please visit the originial BEclear repository.
git clone [email protected]:uds-helms/BEclear-CL.git
cd BEclear-CL
## check and install required packages
Rscript install_requirements.R
chmod +x BEclearCL.RAccessing the help pages:
./BEclearCL.R -hSimple usage example:
./BEclearCL.R -f testDataSet.txt -o testImputed.txt -s testSamples.txtUsing BEclearCL in a pipeline:
cat test.txt | ./BEclearCL.R -wA more detailed description of the tool can be found in the Documentation.pdf.
Akulenko, R., Merl, M., & Helms, V. (2016). BEclear: Batch effect detection and adjustment in DNA methylation data. PLoS ONE, 11(8), 1–17. https://doi.org/10.1371/journal.pone.0159921